I was playing guacamelee the other day and I noticed that they have obvious references to some metroid elements such as chozo statues and metroids themselves. I found it a little weird since the game is for playstation and metroid is Nintendos IP, they even went as far as actually calling their chozo statues "chozo statues", so I found it hard to believe that nintendo would of actually OK-ed it which leads me to question if they even needed permission in the game?

Not only that but what would be the legality of say Saints Row 4 having in their commercial something along the lines of "If you like grand theft auto, you'll love this!!!" or someone making a DR Mario inspired game and promoting it online using a title along the lines of "I made this 3D DR Mario inspired game"

What would be the legality behind mentioning another IP in reference to yours?

It is a fun and exciting area of trademark law called a nominative use.

If you want to refer to something you need to use its name.

Generally it is best to just explicitly name the thing you are referring to and then add in the footnotes somewhere that the thing is a trademark of the other company. If you imply their product you can get in trouble, but simply using the name is generally the best action.

There is a 3-prong test for this:

1) The item cannot be readily identified without using the trademark

2) Usage is limited only to what is necessary for identification

3) The user does not suggest a sponsorship or endorsement

Your examples are correct in that way.

I would have a quick shufti with your lawyer just to make sure you are keeping the use to a minimum, but a comparison between your product and theirs is perfectly legal in most cases. If that is the thing's name, use the name.

There really aren't many cases for it that have run their way through the courts, but these are the two biggest precedents:

The current three-prong test laid out above comes from Playboy v Welles. A former model was featured by the company. The model used the names ("Playboy", "Playmate of the Year", "Playmate of the Month", and "PMOY"). The courts found that her use was legal nominative use. She could use the names of the things simply because those are their names.

Also see Volkswagen v Church. Volkswagen complained that a car dealership extensively advertised that the specialized in "Volkswagen Service" and "VW Service". Notably, he did not use Volkswagen's styles, color schemes, or emblems, just the textual names. He could refer to the names Volkswagen and VW simply because those are their names.